• using R version 4.5.1 (2025-06-13)
• using platform: x86_64-pc-linux-gnu
• R was compiled by     gcc-14 (Debian 14.2.0-19) 14.2.0     GNU Fortran (Debian 14.2.0-19) 14.2.0
• running under: Debian GNU/Linux 13 (trixie)
• using session charset: UTF-8
• checking for file ‘Rmonize/DESCRIPTION’ ... OK
• checking extension type ... Package
• this is package ‘Rmonize’ version ‘1.1.0’
• package encoding: UTF-8
• checking package namespace information ... OK
• checking package dependencies ... OK
• checking if this is a source package ... OK
• checking if there is a namespace ... OK
• checking for executable files ... OK
• checking for hidden files and directories ... OK
• checking for portable file names ... OK
• checking for sufficient/correct file permissions ... OK
• checking serialization versions ... OK
• checking whether package ‘Rmonize’ can be installed ... WARNING Found the following significant warnings:   Note: possible error in 'data_dict_evaluate(dataschema, ': unused argument (as_data_dict_mlstr = TRUE)   Note: possible error in 'dataset_evaluate(dataset = pooled_harmonized_dataset, ': unused argument (as_data_dict_mlstr = as_dataschema_mlstr) See the install log for details. Information on the location(s) of code generating the ‘Note’s can be obtained by re-running with environment variable R_KEEP_PKG_SOURCE set to ‘yes’.
• checking package directory ... OK
• checking for future file timestamps ... OK
• checking ‘build’ directory ... OK
• checking DESCRIPTION meta-information ... OK
• checking top-level files ... OK
• checking for left-over files ... OK
• checking index information ... OK
• checking package subdirectories ... OK
• checking code files for non-ASCII characters ... OK
• checking R files for syntax errors ... OK
• checking whether the package can be loaded ... [2s/3s] OK
• checking whether the package can be loaded with stated dependencies ... [2s/2s] OK
• checking whether the package can be unloaded cleanly ... [2s/2s] OK
• checking whether the namespace can be loaded with stated dependencies ... [2s/2s] OK
• checking whether the namespace can be unloaded cleanly ... [2s/3s] OK
• checking loading without being on the library search path ... [2s/3s] OK
• checking use of S3 registration ... OK
• checking dependencies in R code ... OK
• checking S3 generic/method consistency ... OK
• checking replacement functions ... OK
• checking foreign function calls ... OK
• checking R code for possible problems ... [13s/18s] NOTE dataschema_evaluate: possible error in data_dict_evaluate(dataschema,   taxonomy, as_data_dict_mlstr = TRUE): unused argument   (as_data_dict_mlstr = TRUE) harmonized_dossier_evaluate: possible error in dataset_evaluate(dataset   = pooled_harmonized_dataset, data_dict = dataschema, taxonomy =   taxonomy, as_data_dict_mlstr = as_dataschema_mlstr): unused argument   (as_data_dict_mlstr = as_dataschema_mlstr)
• checking Rd files ... [0s/1s] OK
• checking Rd metadata ... OK
• checking Rd line widths ... OK
• checking Rd cross-references ... NOTE Found the following Rd file(s) with Rd \link{} targets missing package anchors:   harmonized_dossier_summarize.Rd: valueType_list   harmonized_dossier_visualize.Rd: valueType_list Please provide package anchors for all Rd \link{} targets not in the package itself and the base packages.
• checking for missing documentation entries ... OK
• checking for code/documentation mismatches ... OK
• checking Rd \usage sections ... OK
• checking Rd contents ... OK
• checking for unstated dependencies in examples ... OK
• checking contents of ‘data’ directory ... OK
• checking data for non-ASCII characters ... [0s/0s] OK
• checking LazyData ... OK
• checking data for ASCII and uncompressed saves ... OK
• checking installed files from ‘inst/doc’ ... OK
• checking files in ‘vignettes’ ... OK
• checking examples ... [13s/19s] ERROR Running examples in ‘Rmonize-Ex.R’ failed The error most likely occurred in: > base::assign(".ptime", proc.time(), pos = "CheckExEnv") > ### Name: dataschema_evaluate > ### Title: Generate an assessment report for a DataSchema > ### Aliases: dataschema_evaluate > > ### ** Examples > > { + + # use Rmonize_DEMO provided by the package + + library(dplyr) + library(madshapR) # data_dict_filter + + dataschema <- + Rmonize_DEMO$`dataschema - final` %>% + data_dict_filter("name == 'adm_unique_id'") + + dataschema_evaluate(dataschema) + + } Attaching package: ‘dplyr’ The following objects are masked from ‘package:stats’:     filter, lag The following objects are masked from ‘package:base’:     intersect, setdiff, setequal, union Some changes to functions in the current version of madshapR may require updates of existing code. To see which functions have changed, please see https://cran.r-project.org/web/packages/madshapR/news/news.html Error in data_dict_evaluate(dataschema, taxonomy, as_data_dict_mlstr = TRUE) :   unused argument (as_data_dict_mlstr = TRUE) Calls: dataschema_evaluate Execution halted Examples with CPU (user + system) or elapsed time > 5s                      user system elapsed as_dataschema_mlstr 6.534 0.014 8.873
• checking for unstated dependencies in vignettes ... OK
• checking package vignettes ... OK
• checking re-building of vignette outputs ... [6s/9s] OK
• checking PDF version of manual ... [5s/7s] OK
• checking HTML version of manual ... [1s/2s] OK
• checking for non-standard things in the check directory ... OK
• DONE

Status: 1 ERROR, 1 WARNING, 2 NOTEs